Metabolic Strategies Research Articles

Thermal and morphometric correlates of the extremely low rate of energy use in a wild frugivorous primate, the Mayotte lemur

Primates spend on average half as much energy as other placental mammals while expressing a wide range of lifestyles. However, little is known about how primates adapt their rate of energy use in the context of natural environmental variations. Using doubly labelled water, behavioral and accelerometric methods, we measured the total energy expenditure (TEE) and body composition of a population of Eulemur fulvus (N = 12) living in an agroforest in Mayotte. We show that the TEE of this medium-sized cathemeral primate is one of the lowest recorded to date in eutherians. Regression models show that individual variation in the rate of energy use is predicted by fat-free mass, body size, thigh thickness and maximum temperature. TEE is positively correlated with increasing temperature, suggesting that thermoregulation is an important component of the energy budget of this frugivorous species. Mass-specific TEE is only 10% lower than that of a closely related species previously studied in a gallery forest, consistent with the assertion that TEE varies within narrow physiological limits. As lemur communities include many species with unique thermoregulatory adaptations, circadian and/or seasonal temperature variations may have constituted a major selective pressure on the evolution of lemur metabolic strategies.

Metabolic and productive adaptive response of beef cows to successive short-nutritional challenges

This study aimed to analyze the response of lactating beef cows to repeated short nutritional challenges with their performance parameters and plasma metabolites. Multiparous lactating beef cows were subjected to three repeated nutritional challenges in the fourth month of lactation. Each challenge consisted of a 4-d feed restriction (55 % of their average energy and protein requirements), followed by a 3-d refeeding period (100 % requirements). Cows were classified into two groups differing in their performance (milk yield) and metabolic adaptation [non esterified fatty acids (NEFA) and β-hydroxybutyrate (BHB)] to diet changes (metabolic response, MR): High and Low MR cows, where the High MR cows showed a faster and larger response to diet changes than the Low MR cows (P < 0.001). The loss in milk yield during restriction was the smallest in challenge 1 (P < 0.001). Milk urea increased during restriction in challenges 1 and 2 (P < 0.001). The High MR cows had greater NEFA concentrations than their Low MR counterparts during restrictions, and greater BHB concentrations during the restriction of challenge 2 (P < 0.001). Restriction increased NEFA, BHB (only in the High MR cows) and urea (P < 0.01). During refeeding, both milk yield and plasma metabolites recovered basal values (P > 0.05). These results highlight the ability of beef cows to respond to and recover from successive short-term nutrient restrictions, and that despite a certain degree of sensitization of milk yield may have occurred, there were only minimal changes in the metabolic strategies triggered to cope with repeated underfeeding.

Time-resolved multi-omics reveals diverse metabolic strategies of Salmonella during diet-induced inflammation.

With a rise in antibiotic resistance and chronic infection, the metabolic response of Salmonella enterica serovar Typhimurium to various dietary conditions over time remains an understudied avenue for novel, targeted therapeutics. Elucidating how enteric pathogens respond to dietary variation not only helps us decipher the metabolic strategies leveraged for expansion but also assists in proposing targets for therapeutic interventions. In this study, we use a multi-omics approach to identify the metabolic response of Salmonella enterica serovar Typhimurium in mice on both a fibrous diet and high-fat diet over time. When comparing Salmonella gene expression between diets, we found a preferential use of respiratory electron acceptors consistent with increased inflammation in high-fat diet mice. Looking at the high-fat diet over the course of infection, we noticed heterogeneity in samples based on Salmonella ribosomal activity, which is separated into three infection phases: early, peak, and late. We identified key respiratory, carbon, and pathogenesis gene expressions descriptive of each phase. Surprisingly, we identified genes associated with host cell entry expressed throughout infection, suggesting subpopulations of Salmonella or stress-induced dysregulation. Collectively, these results highlight not only the sensitivity of Salmonella to its environment but also identify phase-specific genes that may be used as therapeutic targets to reduce infection.IMPORTANCEIdentifying novel therapeutic strategies for Salmonella infection that occur in relevant diets and over time is needed with the rise of antibiotic resistance and global shifts toward Western diets that are high in fat and low in fiber. Mice on a high-fat diet are more inflamed compared to those on a fibrous diet, creating an environment that results in more favorable energy generation for Salmonella. We observed differential gene expression across infection phases in mice over time on a high-fat diet. Together, these findings reveal the metabolic tuning of Salmonella to dietary and temporal perturbations. Research like this, which explores the dimensions of pathogen metabolic plasticity, can pave the way for rationally designed strategies to control disease.

Computational Strategies to Enhance Cell-Free Protein Synthesis Efficiency

Cell-free protein synthesis (CFPS) has emerged as a powerful tool for protein production, with applications ranging from basic research to biotechnology and pharmaceutical development. However, enhancing the efficiency of CFPS systems remains a crucial challenge for realizing their full potential. Computational strategies offer promising avenues for optimizing CFPS efficiency by providing insights into complex biological processes and enabling rational design approaches. This review provides a comprehensive overview of the computational approaches aimed at enhancing CFPS efficiency. The introduction outlines the significance of CFPS and the role of computational methods in addressing efficiency limitations. It discusses mathematical modeling and simulation-based approaches for predicting protein synthesis kinetics and optimizing CFPS reactions. The review also delves into the design of DNA templates, including codon optimization strategies and mRNA secondary structure prediction tools, to improve protein synthesis efficiency. Furthermore, it explores computational techniques for engineering cell-free transcription and translation machinery, such as the rational design of expression systems and the predictive modeling of ribosome dynamics. The predictive modeling of metabolic pathways and the energy utilization in CFPS systems is also discussed, highlighting metabolic flux analysis and resource allocation strategies. Machine learning and artificial intelligence approaches are being increasingly employed for CFPS optimization, including neural network models, deep learning algorithms, and reinforcement learning for adaptive control. This review presents case studies showcasing successful CFPS optimization using computational methods and discusses applications in synthetic biology, biotechnology, and pharmaceuticals. The challenges and limitations of current computational approaches are addressed, along with future perspectives and emerging trends, such as the integration of multi-omics data and advances in high-throughput screening. The conclusion summarizes key findings, discusses implications for future research directions and applications, and emphasizes opportunities for interdisciplinary collaboration. This review offers valuable insights and prospects regarding computational strategies to enhance CFPS efficiency. It serves as a comprehensive resource, consolidating current knowledge in the field and guiding further advancements.

Metabolic changes associated with PFAS exposure in firefighters: A pilot study

This pilot study investigated the association between occupational exposure to per- and polyfluoroalkyl substances (PFASs) and metabolic profiles among two groups of aviation firefighters (n = 37), with an average of 6 and 31 years of working experience (here referred as junior and senior firefighters) at airports across Australia, with samples collected in 2013. PFAS levels in serum were determined in a previous study to be >17 times higher in the senior firefighter group, reflecting the difference in their occupational exposure to fluorosurfactants among the groups. The aim was to examine metabolic patterns across a broad range of PFAS exposure by comparing metabolic differences and their associations with PFAS levels. In this cross-sectional study, the length of firefighting experience and PFAS levels in serum were both further associated with changes in several classes of metabolites, including free fatty acids, bile acids, amino acids, lipids and metabolites related to gut microbial metabolism. The metabolites associated with the length of firefighting experience showed similarities with the metabolites associated with PFAS levels. A non-monotonic response to PFAS concentrations, particularly in saturated fatty acids, was also observed. In the junior firefighter group, the PFAS concentrations were positively associated with saturated fatty acids, i.e., the saturated fatty acid levels increased with increased PFAS levels. In the senior firefighter group, the trend was opposite, with saturated fatty acids decreasing with increasing levels of PFAS. Accounting for potential confounding factors such as BMI and age could not explain the results. While the study population was small, our results plausibly indicate that PFAS exposure can lead to a metabolic compensation strategy that is disrupted at high, long-term exposures. Our study also suggests that serum metabolites serve as better effect-based markers of the impact of exposure than the traditional clinical measurements alone, such as total triglycerides or total cholesterol.

Regulation of host metabolism and defense strategies to survive neonatal infection

Two distinct defense strategies, disease resistance (DR) and disease tolerance (DT), enable a host to survive infectious diseases. Newborns, constrained by limited energy reserves, predominantly rely on DT to cope with infection. However, this approach may fail when pathogen levels surpass a critical threshold, prompting a shift to DR that can lead to dysregulated immune responses and sepsis. The mechanisms governing the interplay between DR and DT in newborns remain poorly understood. Here, we compare metabolic traits and defense strategies between survivors and non-survivors in Staphylococcus epidermidis (S. epidermidis)-infected preterm piglets, mimicking infection in preterm infants. Compared to non-survivors, survivors displayed elevated DR during the initial phase of infection, followed by stronger DT in later stages. In contrast, non-survivors showed clear signs of respiratory and metabolic acidosis and hyperglycemia, together with exaggerated inflammation and organ dysfunctions. Hepatic transcriptomics revealed a strong association between the DT phenotype and heightened oxidative phosphorylation in survivors, coupled with suppressed glycolysis and immune signaling. Plasma metabolomics confirmed the findings of metabolic regulations associated with DT phenotype in survivors. Our study suggests a significant association between the initial DR and subsequent DT, which collectively contributes to improved infection survival. The regulation of metabolic processes that optimize the timing and balance between DR and DT holds significant potential for developing novel therapeutic strategies for neonatal infection.

The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection.

Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it can serve as a carbon source for P. aeruginosa in the diverse settings that it inhabits. In this study, we evaluate the production and use of two redundant P. aeruginosa L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and ɑ-hydroxybutyrate, which, like lactate, are ɑ-hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays reveal that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosa's success as a resident of contaminated environments and animal hosts.IMPORTANCEPseudomonas aeruginosa is a major cause of lung infections in people with cystic fibrosis, of hospital-acquired infections, and of wound infections. It consumes L-lactate, which is found at substantial levels in human blood and tissues. In this study, we investigated the spatial regulation of two redundant enzymes, called LldD and LldA, which enable L-lactate metabolism in P. aeruginosa biofilms. We uncovered mechanisms and identified compounds that control the preference of P. aeruginosa for LldD versus LldA. We also showed that both enzymes contribute to its ability to survive within macrophages, a behavior that is thought to augment the chronicity and recalcitrance of infections. Our findings shed light on a key metabolic strategy used by P. aeruginosa and have the potential to inform the development of therapies targeting bacterial metabolism during infection.

R-Q@P-D nanoparticle for improving the oral bioavailability and therapeutic efficacy: A novel reversible dual-target-mild-inhibition intestinal metabolic enzymes strategy for resveratrol delivery

The low bioavailability of polyphenols, such as resveratrol (RES), is typically caused by the poor solubility and first-pass effect. To improve bioavailability and reduce adverse effects, an oral reversible UDP-glucuronosyltransferases (UGTs) and sulfotransferases (SULTs) dual-target-mild-inhibition strategy was designed, and a proof-of-concept was studied. This R-Q@P-D nanoparticle for the codelivery of RES and quercetin (QUE) was constructed using pea protein isolate and dipotassium glycyrrhizinate (DG) as nanocarriers. These nanoparticle ingredients were all plant extracts approved by the FDA, and the fabrication process was a simple but novel pH-ultrasonic-shifting method in water conditions. R-Q@P-D exhibited high encapsulation efficiency of RES (97.25 ± 1.13 %) and QUE (94.21 ± 0.62 %), with a uniform nanosize (147.73 ± 1.85 nm). Characterizations implied that RES and QUE could be successfully encapsulated in nanoparticles in amorphous states, and the self-assembly binding between them was non-covalent bonds. Moreover, the in-silicon simulation and experimental results verified interactions between RES and DG, while there was no interaction between QUE and DG. In vivo evaluations showed that R-Q@P-D increased the bioavailability of RES by mildly and reversibly inhibiting intestinal UGTs and SULTs, but without inhibiting hepatic UGTs and SULTs. Moreover, molecular simulations showed that QUE and RES are competitively bound to SULTs but not UGTs. R-Q@P-D had significant therapeutic efficacy and excellent safety performance for its oral application. The tremendous safety and simple fabrication benefited the clinical translation. Together, R-Q@P-D based on reversible UGTs and SULTs dual-target-mild-inhibition strategy might be a promising nano-platform for improving the bioavailability and efficacy of hydrophobic polyphenols.

Physiological and Biochemical Responses of Maize to Elevated CO2 Concentrations: Implications for Growth and Metabolism

Rising atmospheric CO2 levels, a significant consequence of anthropogenic activities, profoundly impact global agriculture and food security by altering plant physiological processes. Despite extensive research, a comprehensive understanding of the specific effects of elevated CO2 on maize (Zea mays L.)’s primary and secondary metabolism remains elusive. This study investigated the responses of maize seedlings cultivated in open-top chambers (OTCs) under three CO2 concentrations: ambient (380 ppm), elevated (600 ppm), and high (1800 ppm). Key growth parameters, including plant height, leaf area, and aboveground biomass (leaf and stem), were assessed alongside metabolic profiles encompassing nonstructural and structural carbohydrates, syringyl (S) and guaiacyl lignin, the syringyl-to-guaiacyl (S/G)-lignin ratio, photosynthetic pigments, total soluble protein, and malondialdehyde (MDA) levels. The results demonstrated that exposure to 600 ppm CO2 significantly enhanced plant height, leaf area, and aboveground biomass compared to ambient conditions. Concurrently, there were notable increases in the concentrations of primary metabolites. In contrast, exposure to 1800 ppm CO2 severely inhibited these growth parameters and induced reductions in secondary metabolites, such as chlorophyll and soluble proteins, throughout the growth stages. The findings underscore the intricate responses of maize metabolism to varying CO2 levels, highlighting adaptive strategies in primary and secondary metabolism under changing atmospheric conditions. This research contributes to a nuanced understanding of maize’s physiological adaptations to future climate scenarios characterized by elevated CO2, with implications for sustainable agriculture and food security.

Combined High-Throughput Proteomics and Random Forest Machine-Learning Approach Differentiates and Classifies Metabolic, Immune, Signaling and ECM Intra-Tumor Heterogeneity of Colorectal Cancer.

Colorectal cancer (CRC) is a frequent, worldwide tumor described for its huge complexity, including inter-/intra-heterogeneity and tumor microenvironment (TME) variability. Intra-tumor heterogeneity and its connections with metabolic reprogramming and epithelial-mesenchymal transition (EMT) were investigated with explorative shotgun proteomics complemented by a Random Forest (RF) machine-learning approach. Deep and superficial tumor regions and distant-site non-tumor samples from the same patients (n = 16) were analyzed. Among the 2009 proteins analyzed, 91 proteins, including 23 novel potential CRC hallmarks, showed significant quantitative changes. In addition, a 98.4% accurate classification of the three analyzed tissues was obtained by RF using a set of 21 proteins. Subunit E1 of 2-oxoglutarate dehydrogenase (OGDH-E1) was the best classifying factor for the superficial tumor region, while sorting nexin-18 and coatomer-beta protein (beta-COP), implicated in protein trafficking, classified the deep region. Down- and up-regulations of metabolic checkpoints involved different proteins in superficial and deep tumors. Analogously to immune checkpoints affecting the TME, cytoskeleton and extracellular matrix (ECM) dynamics were crucial for EMT. Galectin-3, basigin, S100A9, and fibronectin involved in TME-CRC-ECM crosstalk were found to be differently variated in both tumor regions. Different metabolic strategies appeared to be adopted by the two CRC regions to uncouple the Krebs cycle and cytosolic glucose metabolism, promote lipogenesis, promote amino acid synthesis, down-regulate bioenergetics in mitochondria, and up-regulate oxidative stress. Finally, correlations with the Dukes stage and budding supported the finding of novel potential CRC hallmarks and therapeutic targets.

Dual metabolic modification of tumor-targeted bacteria for synergistic chemo-photodynamic therapy and immunotherapy

Conventional anti-tumor methods face challenges such as limited targetability and severe side effects, even when using carrier-assisted delivery of corresponding agents. Additionally, relying on a single modality often leads to an inadequate treatment response. Leveraging the facultative bacteria’s migration tendency to hypoxic tumor tissue and the effectiveness of physicochemical approaches in bacterial engineering, non-pathogenic Escherichia coli MG1655 was metabolically modified for tumor-targeted and synergistic therapy. By taking advantage of the essential D-alanine (D-Ala) component in bacterial peptidoglycan, chemotherapeutic D-Ala-OXA and photosensitizing D-Ala-PPa were firstly prepared and simultaneously labeled on MG1655, creating the multimodal platform (O/P@MG1655). When exposed to red light irradiation, O/P@MG1655 effectively eliminated tumor cells through chemo-photodynamic therapy and induced immunogenic cell death to trigger immunotherapy. Notably, significant inhibition of tumor growth and excellent biosafety were observed in a subcutaneous CT26 mouse tumor model. This dual metabolic modification strategy represents a remarkable advancement in the development of functionalized targeted bacteria for precise tumor treatment.

Dynamic and Static Regulation of Nicotinamide Adenine Dinucleotide Phosphate: Strategies, Challenges, and Future Directions in Metabolic Engineering.

Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a crucial cofactor in metabolic networks. The efficient regeneration of NADPH is one of the limiting factors for productivity in biotransformation processes. To date, many metabolic engineering tools and static regulation strategies have been developed to regulate NADPH regeneration. However, traditional static regulation methods often lead to the NADPH/NADP+ imbalance, causing disruptions in cell growth and production. These methods also fail to provide real-time monitoring of intracellular NADP(H) or NADPH/NADP+ levels. In recent years, various biosensors have been developed for the detection, monitoring, and dynamic regulate of the intracellular NADP(H) levels or the NADPH/NADP+ balance. These NADPH-related biosensors are mainly used in the cofactor engineering of bacteria, yeast, and mammalian cells. This review analyzes and summarizes the NADPH metabolic regulation strategies from both static and dynamic perspectives, highlighting current challenges and potential solutions, and discusses future directions for the advanced regulation of the NADPH/NADP+ balance.

Inverse metabolic engineering based on metabonomics for efficient production of hydroxytyrosol by Saccharomyces cerevisiae

Metabolic engineering provides a powerful approach to efficiently produce valuable compounds, with the aid of emerging gene editing tools and diverse metabolic regulation strategies. However, apart from the current known biochemical pathway information, a variety of unclear constraints commonly limited the optimization space of cell phenotype. Hydroxytyrosol is an important phenolic compound that serves various industries with prominent health-beneficial properties. In this study, the inverse metabolic engineering based on metabolome analysis was customized and implemented to disclose the hidden rate-limiting steps and thus to improve hydroxytyrosol production in Saccharomyces cerevisiae (S. cerevisiae). The potential rate-limiting steps involved three modules that were eliminated individually via reinforcing and balancing metabolic flow, optimizing cofactor supply, and weakening the competitive pathways. Ultimately, a 118.53 % improvement in hydroxytyrosol production (639.84 mg/L) was achieved by inverse metabolic engineering.

Nitrate promotes the growth and the production of short-chain fatty acids and tryptophan from commensal anaerobe Veillonella dispar in the lactate-deficient environment by facilitating the catabolism of glutamate and aspartate.

Veillonella spp. are nitrate-reducing bacteria with anaerobic respiratory activity that reduce nitrate to nitrite. They are obligate anaerobic, Gram-negative cocci that ferment lactate as the main carbon source and produce short-chain fatty acids (SCFAs). Commensal Veillonella reside in the human body site where lactate level is, however, limited for Veillonella growth. In this study, nitrate was shown to promote the anaerobic growth of Veillonella in the lactate-deficient media. We aimed to investigate the underlying mechanisms and the metabolism involved in nitrate respiration. Nitrate (15 mM) was demonstrated to promote Veillonella dispar growth and viability in the tryptone-yeast extract medium containing 0.5 mM L-lactate. Metabolite and transcriptomic analyses revealed nitrate enabled V. dispar to actively utilize glutamate and aspartate from the medium and secrete tryptophan. Glutamate or aspartate was further supplemented to a medium to investigate individual catabolism during nitrate respiration. Notably, nitrate was demonstrated to elevate SCFA production in the glutamate-supplemented medium, and further increase tryptophan production in the aspartate-supplemented medium. We proposed that the increased consumption of glutamate provided reducing power for nitrate respiration and aspartate served as a substrate for fumarate formation. Both glutamate and aspartate were incorporated into the central metabolic pathways via reverse tricarboxylic acid cycle and were linked with the increased production of acetate, propionate, and tryptophan. This study provides further understanding of the promoted growth and metabolic mechanisms by commensal V. dispar utilizing nitrate and specific amino acids to adapt to the lactate-deficient environment.IMPORTANCENitrate is a pivotal ecological factor influencing microbial community and metabolism. Dietary nitrate provides health benefits including anti-diabetic and anti-hypertensive effects via microbial-derived metabolites such as nitrite. Unraveling the impacts of nitrate on the growth and metabolism of human commensal bacteria is imperative to comprehend the intricate roles of nitrate in regulating microbial metabolism, community, and human health. Veillonella are lactate-utilizing, nitrate-reducing bacteria that are frequently found in the human body site where lactate levels are low and nitrate is at millimolar levels. Here, we comprehensively described the metabolic strategies employed by V. dispar to thrive in the lactate-deficient environment using nitrate respiration and catabolism of specific amino acids. The elevated production of SCFAs and tryptophan from amino acids during nitrate respiration of V. dispar further suggested the potential roles of nitrate and Veillonella in the promotion of human health.

MAGs-centric crack: how long will, spore-positive Frankia and most Protofrankia, microsymbionts remain recalcitrant to axenic growth?

Nearly 50 years after the ground-breaking isolation of the primary Comptonia peregrina microsymbiont under axenic conditions, efforts to isolate a substantial number of Protofrankia and Frankia strains continue with enduring challenges and complexities. This study aimed to streamline genomic insights through comparative and predictive tools to extract traits crucial for isolating specific Frankia in axenic conditions. Pangenome analysis unveiled significant genetic diversity, suggesting untapped potential for cultivation strategies. Shared metabolic strategies in cellular components, central metabolic pathways, and resource acquisition traits offered promising avenues for cultivation. Ecological trait extraction indicated that most uncultured strains exhibit no apparent barriers to axenic growth. Despite ongoing challenges, potential caveats, and errors that could bias predictive analyses, this study provides a nuanced perspective. It highlights potential breakthroughs and guides refined cultivation strategies for these yet-uncultured strains. We advocate for tailored media formulations enriched with simple carbon sources in aerobic environments, with atmospheric nitrogen optionally sufficient to minimize contamination risks. Temperature adjustments should align with strain preferences-28-29°C for Frankia and 32-35°C for Protofrankia-while maintaining an alkaline pH. Given potential extended incubation periods (predicted doubling times ranging from 3.26 to 9.60 days, possibly up to 21.98 days), patience and rigorous contamination monitoring are crucial for optimizing cultivation conditions.

Microbial life-history strategies and particulate organic carbon mediate formation of microbial necromass carbon and stabilization in response to biochar addition

Microbial necromass carbon (MNC) contributes significantly to the formation of soil organic carbon (SOC). However, the microbial carbon sequestration effect of biochar is often underestimated and influenced by nutrient availability. The mechanisms associated with the formation and stabilization of MNC remain unclear, especially under the combined application of biochar and nitrogen (N) fertilizer. Thus, in a long-term field experiment (11 years) based on biochar application, we utilized bacterial 16S rRNA gene sequencing, fungal ITS amplicon sequencing, metagenomics, and microbial biomarkers to examine the interactions between MNC accumulation and microbial metabolic strategies under combined treatment with biochar and N fertilizer. We aimed to identify the critical microbial modules and species involved, and to analyze the sites where MNC was immobilized from various components. Biochar application increased the MNC content by 13.9 %. Among the MNC components, fungal necromass contributed more to MNC, but bacteria were more readily enriched after biochar application. The microbial life-history strategies that affected MNC formation under the application of various amounts biochar were linked to the N application level. Under N added at 226.5 kg ha−1, communities such as Actinobacteria and Bacteroidetes with high-growth yield strategies were prevalent and contributed to MNC production. By contrast, under N added at 113.25 kg ha−1 with high biochar application, Proteobacteria with strong resource acquisition strategies were dominant and MNC accumulation was lower. The mineral-associated organic carbon pool was rapidly saturated with the addition of biochar, so the contribution of fungal necromass carbon may have been reduced by reutilization, thereby resulting in the more rapid preservation of bacterial necromass carbon in the particulate organic carbon pool. Overall, our findings indicate that microbial life history traits are crucial for linking microbial metabolic processes to the accumulation and stabilization of MNC, thereby highlighting the their importance for SOC accumulation in farmland soils, and the need to tailor appropriate biochar and N fertilizer application strategies for agricultural soils.

Making the Thermodynamic Cost of Active Inference Explicit.

When describing Active Inference Agents (AIAs), the term "energy" can have two distinct meanings. One is the energy that is utilized by the AIA (e.g., electrical energy or chemical energy). The second meaning is so-called Variational Free Energy (VFE), a statistical quantity which provides an upper bound on surprisal. In this paper, we develop an account of the former quantity-the Thermodynamic Free Energy (TFE)-and its relationship with the latter. We highlight the necessary tradeoffs between these two in a generic, quantum information-theoretic formulation, and the macroscopic consequences of those tradeoffs for the ways that organisms approach their environments. By making this tradeoff explicit, we provide a theoretical basis for the different metabolic strategies that organisms from plants to predators use to survive.

Osmotic stress response of the coral and oyster pathogen Vibrio coralliilyticus: acquisition of catabolism gene clusters for the compatible solute and signaling molecule myo-inositol.

Marine bacteria experience fluctuations in osmolarity that they must adapt to, and most bacteria respond to high osmolarity by accumulating compatible solutes also known as osmolytes. The osmotic stress response and compatible solutes used by the coral and oyster pathogen Vibrio coralliilyticus were unknown. In this study, we showed that to alleviate osmotic stress V. coralliilyticus biosynthesized glycine betaine (GB) and transported into the cell choline, GB, ectoine, dimethylglycine, and dimethylsulfoniopropionate, but not myo-inositol. Myo-inositol is a stress protectant and a signaling molecule that is biosynthesized and used by algae. Bioinformatics identified myo-inositol (iol) catabolism clusters in V. coralliilyticus and other Vibrio, Photobacterium, Grimontia, and Enterovibrio species. Growth pattern analysis demonstrated that V. coralliilyticus utilized myo-inositol as a sole carbon source, with a short lag time of 3 h. An iolG deletion mutant, which encodes an inositol dehydrogenase, was unable to grow on myo-inositol. Within the iol clusters were an MFS-type (iolT1) and an ABC-type (iolXYZ) transporter and analyses showed that both transported myo-inositol. IolG and IolA phylogeny among Vibrionaceae species showed different evolutionary histories indicating multiple acquisition events. Outside of Vibrionaceae, IolG was most closely related to IolG from a small group of Aeromonas fish and human pathogens and Providencia species. However, IolG from hypervirulent A. hydrophila strains clustered with IolG from Enterobacter, and divergently from Pectobacterium, Brenneria, and Dickeya plant pathogens. The iol cluster was also present within Aliiroseovarius, Burkholderia, Endozoicomonas, Halomonas, Labrenzia, Marinomonas, Marinobacterium, Cobetia, Pantoea, and Pseudomonas, of which many species were associated with marine flora and fauna.IMPORTANCEHost associated bacteria such as Vibrio coralliilyticus encounter competition for nutrients and have evolved metabolic strategies to better compete for food. Emerging studies show that myo-inositol is exchanged in the coral-algae symbiosis, is likely involved in signaling, but is also an osmolyte in algae. The bacterial consumption of myo-inositol could contribute to a breakdown of the coral-algae symbiosis during thermal stress or disrupt the coral microbiome. Phylogenetic analyses showed that the evolutionary history of myo-inositol metabolism is complex, acquired multiple times in Vibrio, but acquired once in many bacterial plant pathogens. Further analysis also showed that a conserved iol cluster is prevalent among many marine species (commensals, mutualists, and pathogens) associated with marine flora and fauna, algae, sponges, corals, molluscs, crustaceans, and fish.

Biological Significance of the Komodo Dragon's Tail (Varanus komodoensis, Varanidae).

The Komodo dragon is a unique reptile with an elongated tail that exhibits hitherto unknown adaptations and functions. This tail, composed of 60-86 vertebrae, serves diverse ecological and physiological roles. In juveniles, it is essential for an arboreal lifestyle and balance, while in adults, it functions as a tool for defense and offensive actions. It possesses characteristic haemal arches and a dorsal keel, along with well-developed muscles which enable precise tail control, influencing the Komodo dragon's maneuverability and directional changes. The tail stores adipose tissue, providing Komodo dragons with the ability to regulate body temperature and independence from other seasonal variations. The tail adipose tissue impacts numerous biochemical processes and may play a crucial role in the animals' metabolic strategies and reproductive capabilities. Its functions include providing essential mineral compounds for the organism, such as calcium, phosphorus, magnesium, iron, and zinc. Analysing the biochemical composition of tail fat is crucial for understanding the health of Komodo dragons.

Distinct microbial nitrogen cycling processes in the deepest part of the ocean.

The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.